Week 8: Scratch assay photo analysis using ImageJ
I can’t believe it is already week 8. These past few weeks have passed by so quickly.
This week in particular felt like it went over fast. I kicked off the week productive. I finally figured out how to open the ImageJ program. The download was a zip file and I have never worked with them before, so I had to download a zip extractor to open the software.
After that, I started to focus on the images she gave me. My site advisor gave me a video to watch and follow along with to learn how to use ImageJ and I was able to pick it up fairly quickly. It is not a hard program to use at all. That morning, as I was just starting to use ImageJ, I spent a good three hours working on the first set of Images from the zero-hour time slot of the Scratch assay from last week. I got the hang of the tools that ImageJ had and started making shortcuts by doing sections of pictures at a time to copy data down faster. When I went into the Lab on Monday, my advisor asked me to do three separate time slots that she would be focusing on for the main analysis of the assay. She showed me some of the charts she was planning on creating for the data that I was going to extract. These included different bar graphs and line graphs for the quantity I was measuring, and then some line graphs that she was planning on using when I got a wide variety of time slots done, so she could track that Measurement over time. The first measurement we are using for the analysis of the Assay is the area of the scratch. The way we use this area observed is by looking at the different time slots over time to see how the gap closes and how fast it closes. The scratch assay from last week as mentioned is to measure and replicate the healing process in vivo. So when the cells signal to where they migrate and replicate to close that gap and heal an injury, that is what we are measuring with the area. In the actual program, I have to outline the area of the scratch in 4 different sections because the scratch is a cross scratch where it is one horizontal and vertical scratch on the cell monolayer. Before I can start on each image, I have to calibrate the image editing to the micrometers parameter of each picture. In my case, this is 1000 micrometers for each one. This process was very tedious but very crucial for consistent measurements between each picture.
After the zero-hour set that I completed, I realized that I skipped 4 images, so I had to go back and get the area measurements for those. The main three time slots I was working on for this week were supposed to be 8 hours, 16 hours, and 27 hours. As I was working on the 8-hour pictures, the junior came into the lab to help me. I took a break from my work to try and help her with the program. She didn’t have the same problem with her computer because it was a Mac. After finally opening it on her computer, I taught her how to use the software and went along with the video I received. Her setup was a little different than mine, but I was glad that I was able to teach something that I have learned in the lab after being taught by her many times throughout these past 7 weeks. After that, I continued work in the lab on the images. By the end of the 4 hours in the lab, I was able to complete 3 different time slots(8,16,27 hours). This made me super proud to be able to improve just from the morning to the time that I was working in the lab. The teaching process helped reinforce what I was doing, so that helped me. I only made minor mistakes and didn’t have to go back to analyze images that I skipped.
Since school was out for the Battle of Flowers and Fiesta, I was able to work from home on the last days in the lab. I continued work on the images and have gotten 3 more time slots done. I hope by the beginning of next week, I will be able to finish the area measurements on all time slots.
